Py4CAtS --- Python for Computational ATmospheric Spectroscopy

What's new? (2015-2022)

March 21 --- Summer21 --- Fall 21 --- Winter 21/22 --- Summer 22

July 2015: The 'main' scripts (e.g. lbl2od) can now be used as functions inside the (I)Python interpreter.
October 2015: Sources thoroughly checked with Pep8, PyFlakes, and PyChecker
Script od2ri with function dod2ri added to compute radiation intensity
March 2016: A new function cgs in module cgsUnits.py for easier conversions of physical quantities
Improved ac2wf.py and od2ri functions/modules.
July 2016: Further source code checks with Pylint; Absorption coefficients and optical depths are now stored in subclassed numpy arrays acArray and odArray (similar to xsArray before)
September 2016: Atmospheric data: corrected "CH3CL" -> "CH3Cl"; Functions atlas (in module lines.py), acPlot (in module absCo.py), and odPlot (in module oDepth.py) rewritten (to exploit recursive calls)
October 2016: xs2ac corrected to allow single level atmosphere and cross sections
November 2016: od2ri corrected to allow atmospheric data starting at ToA; Some further checks of 'important' function arguments implemented; srf.py: wavenumber shift implemented in fts function; Atmospheric data sets: trace gas profiles saved in separate file
December 2016: Setup script py4cats.py 'generalized' for Windows (pathname construction!); Line mixing added (first order, Voigt and Lorentz, "brute force" only); read_line_file in the lines.py script now works recursively; atlas now also allows to plot voigtLines; misc.py: new function triSpec for convolution with triangular; moreFun.py: new function erfcx for exponentially scaled complementary error function
May 2017: Function atmPlot now can plot volume mixing ratios (instead of densities), too.
radiance2radiance clean-up
November 2017: New subclassed numpy array for radiance/intensity (i.e. the radiance array along with its attributes): single return variable of function dod2ri.
New function riPlot and updated/adjusted function riSave to plot and save radiance.
New function truncate in module misc.py
January 2018: atmos1D.py:
New function readVMR to read (trace) gas concentration data (i.e. without pressure and temperature);
Function merge_atmos1D can use pure VMR data as second input.
Atmospheric data sets clean-up, reorganized, ...
March 2018: py4cats.py:
Identification / location of path to source files reorganized; wgtFct.py:
(Unix/Linux/...) shell interface adjusted to acArray implementation; lbl2xs.py (and extract.py, hitran.py, geisa.py):
Pressure-induced line shift implemented
June 2018: lines.py --- function atlas: recoded to ensure common wavenumber axis for splitted plots; atmos1D.py: functions merge_atmos1D and regrid updated
Summer 2018: Code ported to Python 3 (the Python 2 code is frozen now!)
October 2018: lbl2xs.py --- a new option cpT to specify the pressure and temperature columns in the pT file
xs2ac.py, ac2od.py, xs2od.py --- new executable scripts to do these steps from the command line (i.e. "wrappers" for the corresponding functions to be called from the command line / (unix) terminal)
extract.py renamed to higstract.py consistent with the main function of this module
December 2018: radInt.py --- new module defining a subclassed array riArray for radiation-intensity, including functions for read, save, and plot
February 2019: Failed matplotlib imports: raise SystemExit errors replaced by print warnings; Module planck.py: new function dPlanck_Wavenumber_dT; Module higstract.py: new method strong for subclassed numpy array lineArray; Module radInt.py: info on spectral response added to legend produced by riPlot; Module wgtFct.py: new method convolve for subclassed numpy array wfArray
March 2019: Module radInt.py: inconsistencies of header comment lines between riSave and riRead removed; Python 2 sources (in directory src2) removed from tarball
April 2019: Broken/incorrect links from bin directory to ../src directory repaired (incorrectly to ../src3); Module srf.py: function Triangle corrected; Demo file corrected: mls=atmos1D(...) ---> mls=atmRead(...)
May 2019: Py4CAtS paper published in Atmosphere 10(5), pp. 262, 2019
May-July 2019: Modules absCo.py, oDepth.py, xSection: old regrid methods removed; Module ac2wf.py: FoV loop in function ac2wf corrected to wfArray; Module atmos1D.py: function cmr with new (second) optional argument what; misc changes in functions atmRead, atmPlot; Module lbl2xs.py: function lbl2xs terminates with non-positive pressure or temperature; Module misc.py: function show_lambda more wavenumbers in NIR added; Module pairTypes.py: class Interval division corrected Python 2 __(r)div__ to Python 3 __(r)truediv__; Module radInt.py: new special method kelvin in class riArray to return equ. brightness temperature; Module wgtFct.py: function wfPlot: contour levels can be set explicitely, axis labels can be suppressed; Cosmetic changes in module ac2wf.py, aeiou.py, srf.py
September 2019 -- January 2020: Module aeiou.py: function loadxyy with new optional argument xLimits; Module cgsUnits: lengthsUnits: ly, pc added; functions lambda2nu, nu2lambda: first argument (wavelengths or wavenumbers) are variable list arguments; Module lineshapes.py: function Rautian now calling hum2wei32 (old: hum1wei24); Module misc.py: function show_lambda with new arguments frmt, yShift, nanometer; Module py4cats.py: import show_lambda added;; Module oDepth.py: functions oDepth_altitudes, oDepth_pressures optionally return altitudes or pressures in km, mb, ....; Module xSection.py: function xsSave: third and fourth arguments swapped (interpolate <--> commentChar)
function xsRead: now can be called recursively
July 2020: Module convolution.py: functions convolveBox, convolveTriangle, convolveGauss: the number of grid points for the new wGrid is now evaluated as int(); Module myMatPlotLib.py: new module with some extra settings; Module py4cats.py: last section with matplotlib settings removed (now in new file myMatPlotLib.py)

March 2021

Source code now reorganized as a package
Source files are now distributed over three subdirectories

lbl: modules related to lbl computations incl. Hitran/Geisa database access, Voigt routines etc.;
art: modules related to atmospheric radiative transfer;
aux: auxiliary modules that should/could be useful in any context, e.g. input/output routines.

The setup module py4cats.py is not required anymore, import of the Py4CAtS modules is now organized by the __init__.py files, in the (I)Python shell simply say
from py4cats import *

Spring - Summer 2021

Plot functions

atmPlot, acPlot, odPlot, riPlot, xsPlot functions have an additional argument **kwArgs (passed thru to MatPlotLib's functions)
acPlot, odPlot, xsPlot with an additional argument xUnit (instead of flag mue or nm)

Module art/ac2od.py:

column density now saved as an additional entry in the odArray instance

Module aux/aerosol.py

new module for aerosol optical depth using simple power law (Angstrom coefficient)

Module lbl/higstract.py

improved/extended support of "beyond Voigt" line parameters in SEOM database

Module aux/ir.ry

added radiusEarth, radiusSun, radiusJupiter, massEarth, massSun, massJupiter

Module lbl/lbl.py

functions lbl_2grids, lbl_3grids: defaults changed to gridRatio=8, lagrange=2;

function lbl_brute: handling/selection of "beyond Voigt" line shapes changed;

function lbl2xs: initial check of `lineshape` modified;

new function init_xSection: setup wavenumber grid (old,original function wavenumber2xs) and zero xs array

Module lbl/lines.py

lineArray class info with better support of "beyond Voigt" parameters;

function xVoigt_parameters with support for "beyond Voigt" parameters (extended version of old `voigt_parameters`);

new function llInfo

Module lbl/lineshapes.py

function argument `S` replaced by `strength`;

function Voigt: call hum1wei32 for tiny y (otherwise hum1wei24);

function Rautian: call hum1wei32 (original hum1wei24);

speed-dependent profiles: now calling sdv and sdr functions (in new module sdr)

Module art/limb.py:

new module for limb (occultation) transmission and effective height

Module lbl/molecules.py

new molecules (hitran20, geisa19/20) added

Module art/oDepth.py

class odArray with new attribute column density;

convolve method with default Gauss;

new function odConvolve (calls class method for a list/dictionary of optical depths);

function odSave with new flag transmission to optionally save exp(-od);

functions oDepth_altitudes, oDepth_pressures can return data in non-cgs units (e.g. km or mb)

Module art/od2ri.py

completely rewritten with added support for surface reflection etc

Module aux/racef.py

new function hum1wei24w;
NOTE: all function except for zpf16p use two real arguments (x,y); zpf16p(z) is used by the sdr module/functions only!

Module art/rayleigh.py

new module for Rayleigh extinction

Module art/radInt.py

class riArray with new method noise;
convolve method with default Gauss;
new function riConvolve (calls class method for a list/dictionary of radiances);
function riRead now returns a dictionary of riArray's if all entries of the pickle file have a `key`;
function riSave: if called with a dictionary of riArray's, save each as dictionary with an extra `key`

Module lbl/sdr.py

new module for speed-dependent Voigt and Rautian functions

Module aux/srf.py

function HyperGauss: bug fix of sqrtLn2**3 ---> sqrtLn2**(1/3); function UltraGauss added

Module aux/struc_array.py

new functions strucArrayChangeName and strucArrayUpdate

Module art/wgtFct.py

function wfPeakHeight now returns altitudes in cm

Fall 2021

Modules art/absCo.py and art/xs2ac.py

acArray attribute molec now saves a dictionary of molecules vs. number densities (old: only (absorbing) molecule names);
this dictionary is set by the xs2ac function and the densities are required by the cia(.py) module/function.

Module lbl/lbl2od.py

three new options for function lbl2od to add cia, Rayleigh, and aerosol extinction to absorption coefficient(s) and optical depth(s)

Module art/cia.py

new module for collision-induced absorption

Winter 2021/22

Module art/atmos1D.py

The function atmPlot can plot all molecular profiles simultaneously with a call atmPlot(atmosData, what='*')

Function _atmosData2cgs: mass density is now removed from atmospheric data.

Module art/oDepth.py

new class method dict for odArray

function _odSave_pickled: redundant code cleaned up by call of odArray.dict class method

function odInfo: now also accepting dictionary of odArrays

Module art/radInt.py

new class methods dict and append for riArray

function _riSave_pickled: redundant code cleaned up by call of riArray.dict class method

function _riRead_pickled: redundant code cleaned up using call to new function dict2riArray

function riConvolve and class method convolve: new wavenumber grid can be set

new function riConcatenate (calling class method riArray.append repeatedly)

Modules lbl/lbl2ac.py and lbl/lbl2od.py

In the corresponding functions a consistency test of atmospheric vs line data has been implemented: stop if line data are given, but no corresponding concentrations

Module aux/misc.py

new function dict_items2groups

Module aux/struc_array.py

new function strucArrayDef

Module aux/pairTypes.py

new class method dict for the three pair classes

Interval initialization more flexible: now also accepts lists, dictionaries (with two elements), and pairs

Numerous modules:

raise SystemExit replaced by more specific raise ValueError etc.

html documentation updated

Spring/Summer 2022

Module art/oDepth.py

new function odSum: alternative implementation of dod2tod
WARNING: slightly different total optical depth (see source file for discussion)

Module aux/convolution.py

convolveBox, convolveTriangle with new option wGrid

convolveGauss with arguments rearranged

Module aux/srf.py

new response function gaussBox

Module aux/euGrid.py

new function gridStep

Module aux/misc.py

new function dict_items2groups

html documentation updated

subdirectories art, aux, lbl corresponding to the package structure